Job ID = 2001547 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 9,012,573 reads read : 9,012,573 reads written : 9,012,573 rm: cannot remove ‘[DSE]RR*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:02:36 9012573 reads; of these: 9012573 (100.00%) were unpaired; of these: 234044 (2.60%) aligned 0 times 7780960 (86.33%) aligned exactly 1 time 997569 (11.07%) aligned >1 times 97.40% overall alignment rate Time searching: 00:02:40 Overall time: 00:02:40 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_rmdupse_core] 3346357 / 8778529 = 0.3812 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Fri, 05 Jul 2019 04:43:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101890/ERX101890.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101890/ERX101890.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101890/ERX101890.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101890/ERX101890.bam'] # control file = None # effective genome size = 2.15e+09 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 05 Jul 2019 04:43:38: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:43:38: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:43:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101890/ERX101890.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101890/ERX101890.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101890/ERX101890.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101890/ERX101890.bam'] # control file = None # effective genome size = 2.15e+09 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 05 Jul 2019 04:43:38: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:43:38: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:43:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101890/ERX101890.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101890/ERX101890.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101890/ERX101890.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101890/ERX101890.bam'] # control file = None # effective genome size = 2.15e+09 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 05 Jul 2019 04:43:39: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:43:39: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:43:47: 1000000 INFO @ Fri, 05 Jul 2019 04:43:47: 1000000 INFO @ Fri, 05 Jul 2019 04:43:48: 1000000 INFO @ Fri, 05 Jul 2019 04:43:56: 2000000 INFO @ Fri, 05 Jul 2019 04:43:56: 2000000 INFO @ Fri, 05 Jul 2019 04:43:56: 2000000 INFO @ Fri, 05 Jul 2019 04:44:04: 3000000 INFO @ Fri, 05 Jul 2019 04:44:05: 3000000 INFO @ Fri, 05 Jul 2019 04:44:05: 3000000 INFO @ Fri, 05 Jul 2019 04:44:12: 4000000 INFO @ Fri, 05 Jul 2019 04:44:13: 4000000 INFO @ Fri, 05 Jul 2019 04:44:13: 4000000 INFO @ Fri, 05 Jul 2019 04:44:20: 5000000 INFO @ Fri, 05 Jul 2019 04:44:21: 5000000 INFO @ Fri, 05 Jul 2019 04:44:22: 5000000 INFO @ Fri, 05 Jul 2019 04:44:24: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:44:24: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:44:24: #1 total tags in treatment: 5432172 INFO @ Fri, 05 Jul 2019 04:44:24: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:44:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 04:44:24: #1 tags after filtering in treatment: 5431870 INFO @ Fri, 05 Jul 2019 04:44:24: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:44:24: #1 finished! INFO @ Fri, 05 Jul 2019 04:44:24: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:44:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:44:25: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:44:25: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:44:25: #1 total tags in treatment: 5432172 INFO @ Fri, 05 Jul 2019 04:44:25: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:44:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 04:44:25: #1 tags after filtering in treatment: 5431870 INFO @ Fri, 05 Jul 2019 04:44:25: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:44:25: #1 finished! INFO @ Fri, 05 Jul 2019 04:44:25: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:44:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:44:26: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:44:26: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:44:26: #1 total tags in treatment: 5432172 INFO @ Fri, 05 Jul 2019 04:44:26: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:44:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 04:44:26: #1 tags after filtering in treatment: 5431870 INFO @ Fri, 05 Jul 2019 04:44:26: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:44:26: #1 finished! INFO @ Fri, 05 Jul 2019 04:44:26: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:44:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:44:26: #2 number of paired peaks: 34612 INFO @ Fri, 05 Jul 2019 04:44:26: start model_add_line... INFO @ Fri, 05 Jul 2019 04:44:26: start X-correlation... INFO @ Fri, 05 Jul 2019 04:44:26: end of X-cor INFO @ Fri, 05 Jul 2019 04:44:26: #2 finished! INFO @ Fri, 05 Jul 2019 04:44:26: #2 predicted fragment length is 147 bps INFO @ Fri, 05 Jul 2019 04:44:26: #2 alternative fragment length(s) may be 3,147 bps INFO @ Fri, 05 Jul 2019 04:44:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101890/ERX101890.10_model.r INFO @ Fri, 05 Jul 2019 04:44:26: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:44:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:44:27: #2 number of paired peaks: 34612 INFO @ Fri, 05 Jul 2019 04:44:27: start model_add_line... INFO @ Fri, 05 Jul 2019 04:44:27: start X-correlation... INFO @ Fri, 05 Jul 2019 04:44:27: end of X-cor INFO @ Fri, 05 Jul 2019 04:44:27: #2 finished! INFO @ Fri, 05 Jul 2019 04:44:27: #2 predicted fragment length is 147 bps INFO @ Fri, 05 Jul 2019 04:44:27: #2 alternative fragment length(s) may be 3,147 bps INFO @ Fri, 05 Jul 2019 04:44:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101890/ERX101890.20_model.r INFO @ Fri, 05 Jul 2019 04:44:27: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:44:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:44:28: #2 number of paired peaks: 34612 INFO @ Fri, 05 Jul 2019 04:44:28: start model_add_line... INFO @ Fri, 05 Jul 2019 04:44:28: start X-correlation... INFO @ Fri, 05 Jul 2019 04:44:28: end of X-cor INFO @ Fri, 05 Jul 2019 04:44:28: #2 finished! INFO @ Fri, 05 Jul 2019 04:44:28: #2 predicted fragment length is 147 bps INFO @ Fri, 05 Jul 2019 04:44:28: #2 alternative fragment length(s) may be 3,147 bps INFO @ Fri, 05 Jul 2019 04:44:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101890/ERX101890.05_model.r INFO @ Fri, 05 Jul 2019 04:44:28: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:44:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:44:45: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:44:46: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:44:48: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:44:56: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101890/ERX101890.10_peaks.xls INFO @ Fri, 05 Jul 2019 04:44:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101890/ERX101890.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:44:56: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101890/ERX101890.20_peaks.xls INFO @ Fri, 05 Jul 2019 04:44:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101890/ERX101890.10_summits.bed INFO @ Fri, 05 Jul 2019 04:44:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101890/ERX101890.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:44:56: Done! INFO @ Fri, 05 Jul 2019 04:44:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101890/ERX101890.20_summits.bed INFO @ Fri, 05 Jul 2019 04:44:57: Done! pass1 - making usageList (36 chroms): 4 millis pass2 - checking and writing primary data (8050 records, 4 fields): 24 millis pass1 - making usageList (80 chroms): 8 millis CompletedMACS2peakCalling pass2 - checking and writing primary data (19948 records, 4 fields): 42 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 04:44:59: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101890/ERX101890.05_peaks.xls INFO @ Fri, 05 Jul 2019 04:44:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101890/ERX101890.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:44:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101890/ERX101890.05_summits.bed INFO @ Fri, 05 Jul 2019 04:44:59: Done! pass1 - making usageList (107 chroms): 10 millis pass2 - checking and writing primary data (29342 records, 4 fields): 49 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。